//
//  Blast.h
//  Cell
//
//  Created by Orbitus on 8/16/07.
//  Copyright 2007 __MyCompanyName__. All rights reserved.
//

#import <Cocoa/Cocoa.h>
#import "iBioCAD_Controller.h"
#import "UnixApp.h"
@interface Blast : UnixApp {

	IBOutlet iBioCAD_Controller *myController;
	
	//BLAST OPTIONS IBOUTLETS
	
    IBOutlet NSWindow *blastWindow;
	IBOutlet NSProgressIndicator *blastRunningIndicator;
	IBOutlet NSArrayController *dnaArrayController;
	IBOutlet NSPopUpButton *programName;
	IBOutlet NSPopUpButton *database;
	IBOutlet NSPopUpButton *alignmentView;
	IBOutlet NSPopUpButton *blastMatrix;
	IBOutlet NSPopUpButton *queryGeneticCodes;	
	IBOutlet NSPopUpButton *databaseGeneticCodes;
	IBOutlet NSTextField *descriptions;
	IBOutlet NSTextField *alignments;
	IBOutlet NSTextField *frameShiftPenalty;
	IBOutlet NSTextField *expect;
	IBOutlet NSTextField *processors;
	IBOutlet NSTextField *bestHitsToKeep;
	IBOutlet NSTextField *largestIntronAllowed;
	IBOutlet NSTextField *mismatchPenalty;
	IBOutlet NSTextField *matchReward;
	IBOutlet NSTextField *costToOpenGap;
	IBOutlet NSTextField *costToExtendGap;
	IBOutlet NSButton *lowComplexityFilter;
	IBOutlet NSButton *htmlOutput;
	IBOutlet NSButton *gappedAlignment;
	IBOutlet NSButton *rpsBlastSearch;
	IBOutlet NSButton *megaBlastSearch;
	IBOutlet NSTextView *blastOutput;
	IBOutlet NSButton *blastButton;
	// ----------
	
	
	NSTask *myBlast;
	NSPipe *pipe;
	NSMutableArray *myArguments;
	
	NSBundle*	myBundle;
	NSString*	myAppPath;
	NSString*	myAppFolderPath;
	NSString*	myBinFolderPath;
	NSString*	myDataFolderPath;
	NSString*	myDesktopFolderPath;
	NSString*	blastPath;
	
	NSManagedObjectContext	*managedObjectContext;
	NSManagedObjectModel	*managedObjectModel;
}
- (IBAction)BLAST:(id)sender;
- (IBAction)TerminateBLAST:(id)sender;

@end
